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  <title>MarvinSketch User Guide</title>
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  <h1>MarvinSketch User's Guide</h1>

  <h2>Table of Contents</h2>

<ul>
<li> <a href="sketch-intro.html">Introduction to MarvinSketch</a></li>
<li> <a href="../applications/install.html">Installation/System Requirements</a></li>
<li> <a href="../applications/msketch.html">Application Instructions</a></li>
<li> <a href="../licensedoc/index.html">License Management</a></li>
<li> <a href="sketch-gui.html">MarvinSketch Graphical User Interface</a></li>
  <ul>
      <li><a href="sketch-gui.html#canvas">Canvas</a></li>
      <li><a href="gui/menubar.html">Menus</a></li>
      <li><a href="gui/toolbars.html">Toolbars</a></li>
      <li><a href="gui/popups.html">Pop-up Menus</a></li>
      <li><a href="gui/statusbar.html">Status Bar</a></li>
      <li><a href="gui/dialogs.html">Dialogs</a></li>
      <li><a href="gui/shortcuts.html">Shortcuts</a></li>
      <li><a href="gui/customization.html">Customizing MarvinSketch</a></li>
      <li><a href="gui/configurations.html">Configurations of MarvinSketch</a></li>
      <li><a href="gui/customization_server_side.html">Customizing MarvinSketch - Server side</a></li>
  </ul>

<li><a href="sketch-basic.html">Basic MarvinSketch Functions</a></li>
<ul>
<li> <a href="../formats/formats.html">File Formats</a></li>
<li> <a href="../datatransfer.html">Cut/Copy/Paste and Drag & Drop Functionality</a></li>
<li><a href="sketch-basic.html#create-molecule">Create a new molecule</a></li>
<li><a href="sketch-basic.html#open-molecule">Open an existing molecule file</a></li>
<li><a href="sketch-basic.html#save-molecule">Save molecule</a></li>
<li><a href="sketch-basic.html#print">Print</a></li>
<li><a href="sketch-basic.html#howto-draw">Drawing structures</a>
  <ul>
        <li><a href="sketch-basic.html#howto-draw.atoms">Atoms</a></li>
        <li><a href="sketch-basic.html#howto-draw.bonds">Bonds</a></li>
        <li><a href="sketch-basic.html#templates">Templates</a></li>
        <li><a href="sketch-basic.html#sprouting">Sprouting</a></li>
        <li><a href="sketch-basic.html#coordination-compounds">Coordination compounds</a></li>
        <li><a href="sketch-basic.html#markush-structures">Markush structures</a></li>
        <li><a href="sketch-basic.html#flip">Flip a molecule</a></li>
        <li><a href="sketch-basic.html#mirror">Mirror a molecule</a></li>
  </ul>
</li>
<li><a href="sketch-basic.html#howto-draw.reactions">Reactions</a></li>
<li><a href="sketch-basic.html#howto-draw.rgroups">Drawing R-group queries</a></li>
<li><a href="sketch-basic.html#howto-draw.sgroups">Drawing groups</a></li>
<li><a href="sketch-basic.html#howto.draw.graphic">Drawing graphics and text boxes</a></li>
<li><a href="sketch-basic.html#howto.draw.linkAtom">Drawing Link atoms</a></li>
<li><a href="sketch-basic.html#howto.select.structure">Selecting structures</a></li>
<li><a href="sketch-basic.html#howto.delete.structure">Deleting structures</a></li>
<li><a href="sketch-basic.html#howto-alter">Working with structures</a>
    <ul>
    <li><a href="sketch-basic.html#edit.visual">Visually editing the structure</a></li>
    <li><a href="sketch-basic.html#edit.source">Editing the Source</a></li>
    <li><a href="sketch-basic.html#clean">Cleaning</a></li>
    <li><a href="sketch-basic.html#aromatic">Aromatic rings</a></li>
    </ul>
</li>
<li><a href="../sci/stereo-doc.html">Stereochemistry</a>
<li><a href="sketch-basic.html#display-structure">Structure Display Options</a>
  <ul>
    <li><a href="sketch-basic.html#move-rotate">Moving and Rotating</a></li>
    <li><a href="sketch-basic.html#scalling">Scaling</a></li>
    <li><a href="sketch-basic.html#format">Molecule Format</a></li>
    <li><a href="sketch-basic.html#molcolor">Colors</a></li>
    <li><a href="sketch-basic.html#implicit-explicit-H">Implicit/Explicit Hydrogens</a></li>
    <li><a href="sketch-basic.html#error-hilight">Error Highlighting</a></li>
  </ul>
</li>
<li><a href="sketch-basic.html#other-windows">Launching 2D and 3D Viewers</a></li>
<li><a href="sketch-basic.html#styles">Customizing structure drawing styles</a></li>

</ul>

<li><a href="sketch-chem.html">Chemical Features of MarvinSketch</a></li>
<ul>
        <li><a href="sketch-chem.html#valence-check">Valence Check</a></li>
        <li><a href="sketch-chem.html#structurechecker">Structure Checker</a></li>
        <li><a href="sketch-chem.html#charges">Charges</a></li>
        <li><a href="sketch-chem.html#reactions">Reactions</a></li>
        <li><a href="sketch-chem.html#mapping">Mapping</a></li>
        <li><a href="sketch-chem.html#isotopes">Isotopes</a></li>
        <li><a href="sketch-chem.html#e-z">E/Z feature</a></li>
	
	<li><a href="sketch-chem.html#sgroups">Abbreviated groups</a></li>
        <li><a href="sketch-chem.html#link-nodes">Link Nodes</a></li>
        <li><a href="sketch-chem.html#groups">Working with Groups</a></li>
        <li><a href="sketch-chem.html#radicals">Working with Radicals</a></li>

        <li><a href="sketch-chem.html#query-guide">Query features</a>
          <ul>
            <li><a href="sketch-chem.html#rgroups">R-groups</a></li>
            <li><a href="sketch-chem.html#atomlist">Atom Lists</a></li>
            <li><a href="sketch-chem.html#notlist">Not Lists</a></li>
            <li><a href="sketch-chem.html#generic-atoms">Generic Atoms</a></li>
            <li><a href="sketch-chem.html#atom-props">Atom Properties</a></li>
            <li><a href="sketch-chem.html#attacheddata">Attached Data</a></li>
           </ul>
        </li>
</ul>

<li><a href="../calculations/calculator-plugins.html">Calculator Plugins</a></li>

<ul>
	<li><a href="../calculations/elemanal.html">Elemental Analysis Plugin</a>
	<li><a href="../calculations/iupacnaming.html">IUPAC Naming Plugin</a>
	<li><a href="../calculations/protonation.html">Protonation</a>
	<ul>
		<li><a href="../calculations/protonation.html#pka">p<i>K</i><sub>a</sub> Plugin</a>
		<li><a href="../calculations/protonation.html#ms">Major Microspecies Plugin</a>
		<li><a href="../calculations/protonation.html#isopoint">Isoelectric Point Plugin</a>
	</ul>
	<li><a href="../calculations/partitioning.html">Partitioning</a>
	<ul>
		<li><a href="../calculations/partitioning.html#logp">log<i>P</i> Plugin</a>
		<li><a href="../calculations/partitioning.html#logd">log<i>D</i> Plugin</a>
	</ul>
        <li><a href="../calculations/chargegroup.html">Charge</a>
	<ul>
		<li><a href="../calculations/chargegroup.html#charge">Charge Plugin</a>
		<li><a href="../calculations/chargegroup.html#polarizability">Polarizability Plugin</a>
		<li><a href="../calculations/chargegroup.html#oen">Orbital Electronegativity Plugin</a>
	</ul>
	<li><a href="../calculations/isomers.html">Isomers</a>
	<ul>
		<li><a href="../calculations/isomers.html#tautomer">Tautomerization Plugin</a>
		<li><a href="../calculations/isomers.html#resonance">Resonance Plugin</a>
		<li><a href="../calculations/isomers.html#stereoisomer">Stereoisomer Plugin</a>
	</ul>
	<li><a href="../calculations/conformation.html">Conformation</a>
	<ul>
		<li><a href="../calculations/conformation.html#conformer">Conformer Plugin</a>
		<li><a href="../calculations/conformation.html#moldyn">Molecular Dynamics Plugin</a>
	</ul>
	<li><a href="../calculations/geometrygroup.html">Geometry</a>
	<ul>
		<li><a href="../calculations/geometrygroup.html#topolanal">Topology Analysis Plugin</a>
		<li><a href="../calculations/geometrygroup.html#geometry">Geometry Plugin</a>
		<li><a href="../calculations/geometrygroup.html#TPSA">Polar Surface Area Plugin (2D)</a>
		<li><a href="../calculations/geometrygroup.html#MSA">Molecular Surface Area Plugin (3D)</a>
	</ul>
        <li><a href="../calculations/markush.html">Markush Enumeration Plugin</a></li>
	<li><a href="../calculations/other.html">Other</a>
	<ul>
		<li><a href="../calculations/other.html#HBDA">Hydrogen Bond Donor-Acceptor Plugin</a>
		<li><a href="../calculations/other.html#huckel">Huckel Analysis Plugin</a>
		<li><a href="../calculations/other.html#refractivity">Refractivity Plugin</a>
	</ul>
        <li><a href="../calculations/Validations.html">Test Results</a></li>
	<li><a href="../calculations/references.html">References</a></li>
</ul>

<li><a href="../acknowledgements.html">Acknowledgements</a></li>
</ul>


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<p>
<a href="../index.html">Marvin User's Guide</a>
</p>
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Copyright &copy; 1998-2010
<a HREF="http://www.chemaxon.com">ChemAxon Ltd.</a>
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<a HREF="http://www.chemaxon.com/marvin/">http://www.chemaxon.com/marvin</a>
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